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- PDB-2fgj: Crystal structure of the ABC-cassette H662A mutant of HlyB with b... -

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Basic information

Entry
Database: PDB / ID: 2fgj
TitleCrystal structure of the ABC-cassette H662A mutant of HlyB with bound ATP
ComponentsAlpha-hemolysin translocation ATP-binding protein hlyB
KeywordsTRANSPORT PROTEIN / ABC-transporter / ATPase / composite dimer
Function / homology
Function and homology information


type I protein secretion system complex / protein secretion by the type I secretion system / ABC-type oligopeptide transporter activity / peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
ATPase, type I secretion system, HlyB / Peptidase C39-like A / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily ...ATPase, type I secretion system, HlyB / Peptidase C39-like A / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Alpha-hemolysin translocation ATP-binding protein HlyB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZaitseva, J. / Oswald, C. / Jumpertz, T. / Jenewein, S. / Holland, I.B. / Schmitt, L.
CitationJournal: Embo J. / Year: 2006
Title: A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer.
Authors: Zaitseva, J. / Oswald, C. / Jumpertz, T. / Jenewein, S. / Wiedenmann, A. / Holland, I.B. / Schmitt, L.
History
DepositionDec 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-hemolysin translocation ATP-binding protein hlyB
B: Alpha-hemolysin translocation ATP-binding protein hlyB
C: Alpha-hemolysin translocation ATP-binding protein hlyB
D: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7728
Polymers110,7434
Non-polymers2,0294
Water3,531196
1
A: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1932
Polymers27,6861
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1932
Polymers27,6861
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1932
Polymers27,6861
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-hemolysin translocation ATP-binding protein hlyB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1932
Polymers27,6861
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.558, 195.166, 63.288
Angle α, β, γ (deg.)90.00, 110.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alpha-hemolysin translocation ATP-binding protein hlyB


Mass: 27685.781 Da / Num. of mol.: 4 / Fragment: amino acids 467-707 / Mutation: H662A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hlyB / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P08716
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium malonate, PEG 5500-MME, sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 25379 / Num. obs: 24465 / % possible obs: 96.4 % / Redundancy: 10.2 % / Rsym value: 0.057
Reflection shellResolution: 2.6→2.65 Å / Rsym value: 0.193 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1XEF

1xef


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.914 / SU B: 29.43 / SU ML: 0.336 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 3.2 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27936 1298 5 %RANDOM
Rwork0.20778 ---
obs0.21147 24465 96.4 %-
all-25738 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.404 Å2
Baniso -1Baniso -2Baniso -3
1-4.53 Å20 Å2-0.07 Å2
2---0.36 Å20 Å2
3----4.22 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7552 0 124 196 7872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227788
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.9810540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.18424.138348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.915151432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3851564
X-RAY DIFFRACTIONr_chiral_restr0.0690.21208
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025720
X-RAY DIFFRACTIONr_nbd_refined0.1990.23819
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2346
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.28
X-RAY DIFFRACTIONr_mcbond_it0.2761.54942
X-RAY DIFFRACTIONr_mcangle_it0.49227708
X-RAY DIFFRACTIONr_scbond_it0.55233206
X-RAY DIFFRACTIONr_scangle_it0.9254.52832
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 103
Rwork0.273 2157
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4592-0.0388-0.40574.99350.40957.271-0.10050.47230.3436-0.72790.13790.25820.1077-0.1774-0.03740.4174-0.0507-0.06930.47280.0350.4537-1.85441.4923-10.2674
22.610.47770.25774.0259-0.55044.85520.192-0.727-0.00640.6615-0.04320.147-0.17-0.1412-0.14870.4719-0.10560.05450.6256-0.02350.4269-0.8004-2.923122.389
33.1553-0.0108-0.76095.14130.80369.21850.3256-0.44550.0950.6088-0.0709-0.43820.23390.3856-0.25460.3872-0.0831-0.11710.5045-0.02450.469925.445456.766420.2851
44.53710.192-0.57684.9654-0.10169.7171-0.34010.728-0.6766-1.0180.3538-0.3907-0.4524-0.0207-0.01370.6482-0.17770.17030.4883-0.18550.546526.586548.6938-11.6526
55.88981.2520.11569.7221.54677.1694-0.10610.28270.33310.1238-0.1891-0.1364-0.73660.4210.29520.4715-0.109-0.02290.28310.00230.54535.640218.98257.2074
68.1815-3.062.58587.8011-1.981213.76780.2980.26570.1809-0.0153-0.3847-0.98450.86611.81310.08660.43160.12630.0430.45140.01130.454712.9847-15.52834.8674
75.3857-3.1171-0.427611.5986-3.95997.12120.24210.0942-0.4335-1.2008-0.36371.0412-0.1574-0.85170.12170.54120.1647-0.07250.41420.02140.456910.518666.26641.7722
86.35683.5049-0.3359.1179-2.10387.2391-0.12370.1521-0.44870.49650.0663-0.68070.5302-0.09480.05740.3946-0.0149-0.05840.2346-0.0530.582721.193232.87487.9692
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA467 - 5497 - 89
2X-RAY DIFFRACTION1AA624 - 707164 - 247
3X-RAY DIFFRACTION2BB467 - 5497 - 89
4X-RAY DIFFRACTION2BB624 - 707164 - 247
5X-RAY DIFFRACTION3CC467 - 5497 - 89
6X-RAY DIFFRACTION3CC624 - 707164 - 247
7X-RAY DIFFRACTION4DD467 - 5497 - 89
8X-RAY DIFFRACTION4DD624 - 707164 - 247
9X-RAY DIFFRACTION5AA550 - 62390 - 163
10X-RAY DIFFRACTION6BB550 - 62390 - 163
11X-RAY DIFFRACTION7CC550 - 62390 - 163
12X-RAY DIFFRACTION8DD550 - 62390 - 163

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